DNA supercoiling facilitates the site juxtaposition of two distal DNA sites by slithering opposing segments of the interwound superhelix or bending DNA to coil[1]}, [2]}, [3]}, [4]}, it then promotes protein binding or enhance the gene expression[5]}, [6]}, [7]}.
As we have seen, slithering motion of the segments in a plectomeic helix is accompanied with plectoneme diffusion. However, the diffusion may not offer an efficient mechanism for site juxtaposition. An efficient mechanism for achieving site juxtaposition is combining plectoneme diffusion and hopping. These mechanisms can be efficiently explored by employing the two phase dynamics of the DNA supercoiling which is physical justified and computationally trivial.
